Isolation and characterization of Phanerochaete chrysosporium mutants resistant to antifungal compounds Duy Vuong Nguyen To cite this version: Duy Vuong Nguyen. Isolation and characterization of Phanerochaete chrysosporium mutants resistant to antifungal compounds. Mycology. Université de Lorraine, 2020. English. NNT : 2020LORR0045. tel-02940144 HAL Id: tel-02940144 https://hal.univ-lorraine.fr/tel-02940144 Submitted on 16 Sep 2020 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. AVERTISSEMENT Ce document est le fruit d'un long travail approuvé par le jury de soutenance et mis à disposition de l'ensemble de la communauté universitaire élargie. Il est soumis à la propriété intellectuelle de l'auteur. Ceci implique une obligation de citation et de référencement lors de l’utilisation de ce document. D'autre part, toute contrefaçon, plagiat, reproduction illicite encourt une poursuite pénale. Contact : [email protected] LIENS Code de la Propriété Intellectuelle. articles L 122. 4 Code de la Propriété Intellectuelle. articles L 335.2- L 335.10 http://www.cfcopies.com/V2/leg/leg_droi.php http://www.culture.gouv.fr/culture/infos-pratiques/droits/protection.htm Ecole Doctorale SIReNa (Sciences et Ingénierie des Ressources Naturelles) Thèse Présentée et soutenue publiquement pour l’obtention du titre de DOCTEUR DE l’UNIVERSITE DE LORRAINE Mention « Biologie et écologie des forêts et des agrosystèmes » Par Duy Vuong NGUYEN Isolation et caractérisation de mutants de Phanerochaete chrysosporium résistants à différents composés antifongiques Soutenance le 3 Juin 2020 Membres du jury : Rapporteurs : Mme. Catherine RAFIN MCF, Université du Littoral Côte d’Opale M. Christian MEYER DR, INRAE, Versailles Examinateurs : Mme. Harivony RAKOTOARIVONINA MCF, Université de Reims M. Philippe GÉRARDIN Pr, Université de Lorraine M. Éric GELHAYE DR, INRAE Nancy, Directeur de thèse M. Rodnay SORMANI MCF, Université de Lorraine, Co-directeur de thèse Invités : Mme. Nadine AMUSANT Chargée de Recherche, CIRAD ACKNOWLEGEMENTS First of all, I would like to thank the members of the thesis committee, Catherine Rafin, Christian Meyer, Harivony Rakotoarivonina, Nadine Amusant, and Philippe Gérardin for agreeing to read this manuscript and evaluate my thesis work. The research was carried out at the team Stress Response and Redox Regulation (Redox team), UMR 1136 laboratory at the University of Lorraine where my work was supported by Laboratory of Interactions between Plants and Microorganisms (IAM). This support is warmly acknowledged. I would like to sincerely thank the Vietnam Ministry of Agriculture and Rural Development, Vietnam Ministry of Education and Training, France embassy at Hanoi, and Campus France for the scholarship and supports during my studies in France. I would also like to thank the Lab of Excellence ARBRE for funding to the project ANR-11-LABX-0002-01 that provides materials for my studies. I am very grateful to my supervisors, Professor Eric Gelhaye and co-supervisor A. Professor Rodnay Sormani, for your valuable guidance and supports during my study and for me a chance and freedom to explore the physiology of filamentous fungi (regulatory and signaling proteins) due to I only studied biochemistry as a branch of physical science in previously. Thank both for reading, providing critical comments, and giving me ideas to improve my thesis manuscript, that is a very big work, and I know that it took so much time of yours. Thank Eric so much for your financial support to my travel to the ECFG14th in Israel, a very big international congress on fungal biology. I consider myself very lucky to work with you as my thesis supervisor. Sincerely, thank Eric and Rodnay for everything. I warmly thank Professor Jean-Pierre who read carefully my thesis and give me useful comments and suggestions, and also for supporting me English improvement as other PhD students of Redox team during our working time at here. I also wish to thank Professors Nicolas Rouhier and Mélanie Rouhier, leaders of Redox team who keep weekly seminars. I have obtained not only so much knowledge on plant biochemistry and fungal physiology but also slides preparation and presentation skills from those seminars. Thank Nicolas also for reminding all people to organize workspace of the laboratory as cultural space, it is not easy to find a space as here. Special thanks to Elena, who always motivates me through your bits of help in both work and life. I always remember images we talked on the way coming back home together in many times, they will be importantly memorable of mine. Special thanks also to Mélanie and Flavian, who started PhD course with me. Both always have paid attention so much to my work, especially during writing the thesis manuscript, which was a very difficult period. Your supportive attitude towards my work is very important. Thanks to your sincere inspirations, I had got more motivation for working. I would like to thank many colleagues and friends who I have had the pleasure of working during the years for the very open and friendly space in the laboratory. Those include Jérémy, Arnaud, Tiphaine, Benjamin Petre, Benjamin Selles, Jean-Michel, Julien, Muriel, Alexis, Raphael, Fanny, Elodie, Nicolas Valette, Anna, Jonathan, Thomas, Antonio, Delphine, Damien, Loïck, Marion, Kevin, Corrine, and Martine. I also would like to warmly thank all the administrative staff of the Doctoral Register office, the School of RP2E and SIReNa, for the information necessary for my study activities and also for their aides when I have several issues. Warm thanks are sent to all my Vietnamese friends for helping me to keep spirits and motivation, also to find a solution for the difficulties and problems I met. Finally, I feel especially lucky to have such a wonderful family. My parents, my wife Anh Thu, and my daughter Minh Thai always inspire me to have confident thoughts. Thank you all for your love and support. I know that all of the achievements I have obtained here belongs to you. TABLE OF CONTENTS ABBREBRIATIONS RÉSUMÉ INTRODUCTION I. Fungal adaptation to environment .................................................................................................................. 1 I.1 Fungi have to adapt to their environment ................................................................................................ 1 I.2 Fungal sensing of the environment ............................................................................................................... 5 I.2.1 Nutrient sensing ................................................................................................................................................. 6 Carbon sensing ............................................................................................................................................................. 6 Carbon nutrient sensing and responses in lignocellulose degradation ............................................. 11 Nitrogen sensing ....................................................................................................................................................... 13 Target Of Rapamycin (TOR) signaling as a key regulator of growth in the adaptation of filamentous fungi ...................................................................................................................................................... 15 I.2.2 Stress sensing and responses for adaptation to environment ..................................................... 18 II. Wood and wood degrading fungi .................................................................................................................. 22 II.1 Wood components ............................................................................................................................................. 22 II.1.1 Structural compositions ............................................................................................................................. 25 II.1.1 Cellulose .............................................................................................................................. 25 II.1.2 Hemicellulose ..................................................................................................................... 25 II.1.3 Lignin .................................................................................................................................. 27 II.I.2 Wood extractives ............................................................................................................................................ 27 II.I.2.1 Phenolic compounds ....................................................................................................... 28 II.I.2.1.1 Flavonoids ..................................................................................................................... 29 II.I.2.1.2 Tannins .......................................................................................................................... 31 II.I.2.1.3 Stilbenes .......................................................................................................................